diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py index 0ccb02ad0..195706610 100644 --- a/fmriprep/cli/parser.py +++ b/fmriprep/cli/parser.py @@ -635,6 +635,13 @@ def _slice_time_ref(value, parser): dest='run_reconall', help='Disable FreeSurfer surface preprocessing.', ) + g_fs.add_argument( + '--fs-no-resume', + action='store_true', + dest='fs_no_resume', + help='EXPERT: Import pre-computed FreeSurfer reconstruction without resuming. ' + 'The user is responsible for ensuring that all necessary files are present.', + ) g_carbon = parser.add_argument_group('Options for carbon usage tracking') g_carbon.add_argument( diff --git a/fmriprep/config.py b/fmriprep/config.py index e01acec98..08fbb51ce 100644 --- a/fmriprep/config.py +++ b/fmriprep/config.py @@ -573,6 +573,8 @@ class workflow(_Config): """Run *fieldmap-less* susceptibility-derived distortions estimation.""" hires = None """Run FreeSurfer ``recon-all`` with the ``-hires`` flag.""" + fs_no_resume = None + """Adjust pipeline to reuse base template of existing longitudinal freesurfer""" ignore = None """Ignore particular steps for *fMRIPrep*.""" level = None diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py index 584a60e88..df3268a5d 100644 --- a/fmriprep/workflows/base.py +++ b/fmriprep/workflows/base.py @@ -321,6 +321,7 @@ def init_single_subject_wf(subject_id: str): output_dir=fmriprep_dir, freesurfer=config.workflow.run_reconall, hires=config.workflow.hires, + fs_no_resume=config.workflow.fs_no_resume, longitudinal=config.workflow.longitudinal, msm_sulc=msm_sulc, t1w=subject_data['t1w'],